Accurate, multi-kb reads resolve complex populations and detect rare microorganisms (Q35238274)

7 August 2017

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms (English)

1 reference

7 August 2017

1

1 reference

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2 June 2020

David Burstein

9

1 reference

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2 June 2020

Susannah G. Tringe

10

1 reference

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2 June 2020

Kenneth H. Williams

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25665577%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Jillian Banfield

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25665577%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

3

Laura A Hug

1 reference

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2 June 2020

author name string

Michael Kertesz

2

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2 June 2020

Dmitry Pushkarev

4

1 reference

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2 June 2020

Timothy A Blauwkamp

5

1 reference

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2 June 2020

Cindy J Castelle

6

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2 June 2020

Mojgan Amirebrahimi

7

1 reference

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2 June 2020

Brian C Thomas

8

1 reference

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2 June 2020

publication date

9 February 2015

1 reference

7 August 2017

1 reference

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2 June 2020

volume

25

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2 June 2020

issue

4

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2 June 2020

page(s)

534-543

1 reference

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Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements

2 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Tackling soil diversity with the assembly of large, complex metagenomes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Whole-genome haplotyping using long reads and statistical methods

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Insights into the phylogeny and coding potential of microbial dark matter

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

The genome sequence of the colonial chordate, Botryllus schlosseri

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Ray Meta: scalable de novo metagenome assembly and profiling.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Fast gapped-read alignment with Bowtie 2

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Joint analysis of multiple metagenomic samples

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Search and clustering orders of magnitude faster than BLAST

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Glycoside hydrolases: catalytic base/nucleophile diversity

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Prodigal: prokaryotic gene recognition and translation initiation site identification

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Community-wide analysis of microbial genome sequence signatures

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Community structure and metabolism through reconstruction of microbial genomes from the environment

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

An efficient algorithm for large-scale detection of protein families

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

A whole-genome assembly of Drosophila

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Prokaryotes: the unseen majority

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Structures and mechanisms of glycosyl hydrolases

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

A general method applicable to the search for similarities in the amino acid sequence of two proteins

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Basic local alignment search tool

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381525

26 September 2018

Identifiers

DOI

10.1101/GR.183012.114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25665577%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

1 reference

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2 June 2020

1 reference

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